The phrase "alignment to include the" is correct and usable in written English.
It can be used in contexts where you are discussing the need for alignment in a process, project, or strategy that involves including specific elements or components.
Example: "The team is working on an alignment to include the necessary resources for the upcoming project."
Alternatives: "alignment to incorporate the" or "alignment to encompass the".
As the local algorithm of BLAST does not extend the alignment to include terminal mismatches (e.g., U C), proteins ending with an Sec can escape identification by the standard search methods.
This clarification of the model for euAP3 evolution has been facilitated by the greatly improved sampling of basal eudicot lineages, which, in turn, allowed the refinement of the AP3 alignment to include fewer indels than that used by Vandenbussche et al. [ 22].
Therefore, the search for the best alignment option has to include the neighboring syllables.
Alignments were trimmed to include the region 50 bp downstream from the TSS and 1000 bp upstream, a region that should encompass the majority of proximal promoter regulatory elements associated with a given gene [57].
Phylogenetic analyses based on 83-gene and inverted repeat region alignments, the largest sequence-rich datasets to include the basal eudicot family Proteaceae, provide strong support for a Proteales clade that includes Macadamia, Platanus and Nelumbo.
Because some sequences were limited in length, the final worldwide ON1 alignment was trimmed to include only the C-terminal G gene region over the terminal 333 nt.
For each query sequence, the EST alignments were filtered to include only the ESTs with a sequence identity of greater or equal to 90% and an alignment length of 30 or more residues.
The conservation threshold corresponds to the minimum percentage of columns, from the original alignment, which the user wants to include in the trimmed alignment.
Even though the PAML4 individual ancestor is the shortest, it is Mega5 that has left out the very most highly conserved region of the alignment when asked to include 100% of the MSA.
For the analysis of each intron alignment, the tree was pruned to include only the species found in that alignment.
